sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 5jj0 | SAM | Histone-lysine N-methyltransferase EHMT2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5jj0 | SAM | Histone-lysine N-methyltransferase EHMT2 | / | 1.000 | |
| 5jhn | SAM | Histone-lysine N-methyltransferase EHMT2 | / | 0.773 | |
| 2o8j | SAH | Histone-lysine N-methyltransferase EHMT2 | / | 0.656 | |
| 5jin | SAM | Histone-lysine N-methyltransferase EHMT2 | / | 0.636 | |
| 3hna | SAH | Histone-lysine N-methyltransferase EHMT1 | / | 0.596 | |
| 3mo0 | SAH | Histone-lysine N-methyltransferase EHMT1 | / | 0.594 | |
| 5czy | SAM | Eukaryotic huntingtin interacting protein B | / | 0.555 | |
| 2rfi | SAH | Histone-lysine N-methyltransferase EHMT1 | / | 0.538 | |
| 3kmt | SAH | Histone H3K27 methylase | / | 0.536 | |
| 2h21 | SAM | Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic | 2.1.1.127 | 0.535 | |
| 3pdn | SFG | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.528 | |
| 3cbp | SFG | Histone-lysine N-methyltransferase SETD7 | 2.1.1.43 | 0.524 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.505 | |
| 1mlv | SAH | Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic | 2.1.1.127 | 0.502 | |
| 3ru0 | SFG | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.502 | |
| 3swc | SAH | Histone-lysine N-methyltransferase EHMT1 | / | 0.499 | |
| 4j83 | SAM | Histone-lysine N-methyltransferase SETD7 | 2.1.1.43 | 0.498 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.492 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.491 | |
| 4o30 | SAH | Probable Histone-lysine N-methyltransferase ATXR5 | 2.1.1.43 | 0.489 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.487 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.487 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.485 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.484 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.483 | |
| 3n71 | SFG | Histone-lysine N-methyltransferase Smyd1 | / | 0.479 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.478 | |
| 3rib | SAH | N-lysine methyltransferase SMYD2 | / | 0.476 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.475 | |
| 3ooi | SAM | Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific | 2.1.1.43 | 0.474 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 5ex0 | SAH | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.472 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.470 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.469 | |
| 4nv1 | 4TG | Formyl transferase | / | 0.469 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.468 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.468 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 4fs4 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 4ype | SAM | Histone-lysine N-methyltransferase ASH1L | 2.1.1.43 | 0.467 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.466 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.466 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.465 | |
| 4djw | 0KP | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 4usq | FAD | Pyridine nucleotide-disulfide oxidoreductase | / | 0.462 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.461 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.461 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.461 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.461 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.460 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.460 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.460 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.460 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.459 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.459 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.458 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.458 | |
| 3pz2 | 3PZ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.458 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.458 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.457 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 1vjt | NAD | Alpha-glucosidase, putative | / | 0.456 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3tg4 | SAM | N-lysine methyltransferase SMYD2 | / | 0.456 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.456 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.456 | |
| 4j0z | 1H5 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.455 | |
| 2bqz | SAH | N-lysine methyltransferase KMT5A | / | 0.455 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3ioe | A7D | Pantothenate synthetase | 6.3.2.1 | 0.455 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.455 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.455 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.454 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 4jpe | 1M7 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4qen | SAH | Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 | 2.1.1.43 | 0.454 | |
| 4ypu | SAM | Histone-lysine N-methyltransferase ASH1L | 2.1.1.43 | 0.454 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.453 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.453 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.453 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.453 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.453 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.452 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.452 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.452 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.452 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.451 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.451 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.451 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.451 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.451 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4dyn | 0MR | Nucleoprotein | / | 0.451 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.450 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.450 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.449 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.449 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.449 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.449 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.449 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.449 | |
| 5cfl | C2E | Stimulator of interferon genes protein | / | 0.449 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.448 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.448 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.448 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.447 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 2xyt | TC9 | Soluble acetylcholine receptor | / | 0.447 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.447 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.447 | |
| 3qfr | FAD | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.447 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4cth | RDF | Neprilysin | / | 0.447 | |
| 4qg1 | DTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.447 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.446 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.446 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4usr | FAD | Monooxygenase | / | 0.446 | |
| 4wdg | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.446 | |
| 4y0k | NAP | AntE | / | 0.446 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.445 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.445 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.445 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.445 | |
| 4asu | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.445 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.445 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.445 | |
| 4nv1 | TYD | Formyl transferase | / | 0.445 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 1zzu | DP1 | Nitric oxide synthase, brain | 1.14.13.39 | 0.444 | |
| 2g94 | ZPQ | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2hld | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.444 | |
| 2hld | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.444 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.444 | |
| 3bj7 | COA | Diamine acetyltransferase 1 | / | 0.444 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.444 | |
| 4ke0 | 1R8 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.444 | |
| 4ypa | SAM | Histone-lysine N-methyltransferase ASH1L | 2.1.1.43 | 0.444 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.443 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.443 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.443 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.443 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.443 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.443 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.443 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4j0t | 6T9 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.443 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.442 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.442 | |
| 2xfy | ACX | Beta-amylase | 3.2.1.2 | 0.442 | |
| 3c34 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.442 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.442 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.442 | |
| 5hq8 | SAH | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.442 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.441 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.441 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.441 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.441 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.441 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.441 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.441 | |
| 4o6f | SAH | N-lysine methyltransferase SMYD2 | / | 0.441 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.440 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1j36 | LPR | Angiotensin-converting enzyme | 3.4.15.1 | 0.440 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3l3l | L3L | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.440 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.440 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.440 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4bub | ADP | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase | / | 0.440 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.440 |